› 4fir

X-ray diffraction
3.1Å resolution

Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus

Released:
DOI: 10.2210/pdb4fir/pdb
PDB entry 4fir coloured by chain, front view.
PDB entry 4fir coloured by chain, side view.
PDB entry 4fir coloured by chain, top view.
Source organism: Pyrococcus horikoshii OT3
Primary publication:
Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus horikoshii.
Matsuura A, Yoon JY, Yoon HJ, Lee HH, Suh SW
Mol Cells 34 407-12 (2012)
PMID: 23104439

Function and Biology Details

Reaction catalysed: 
(1a) L-glutamine + H(2)O = L-glutamate + NH(3)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129804 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyridoxal 5'-phosphate synthase subunit PdxS Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 335 amino acids
Theoretical weight: 37.07 KDa
Source organism: Pyrococcus horikoshii OT3
Expression system: Escherichia coli
UniProt:
  • Canonical: O59080 (Residues: 1-335; Coverage: 100%)
Gene names: PH1355, pdxS
Sequence domains:
Structure domains: Aldolase class I

Ligands and Environments

1 bound ligand:
Ligand R5P 6 x R5P
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P21
Unit cell:
a: 59.165Å b: 179.065Å c: 109.359Å
α: 90° β: 102.53° γ: 90°
R-values:
R R work R free
0.187 0.185 0.227
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Structural Dynamics and Perspectives of Vitamin B6 Biosynthesis Enzymes in Plasmodium: Advances and Open Questions.
Barra et al. (2021)
3 other articles

2 mentions without citation

Structural definition of the lysine swing in Arabidopsis thaliana PDX1: Intermediate channeling facilitating vitamin B6 biosynthesis.
Robinson et al. (2016)
1 more